Locus 1838

Sequence ID	3R_DroMel_CAF1
Location	5,271,483 – 5,271,628
Length	145
Max. P	0.943254

overview

Window 0

Location	5,271,483 – 5,271,603
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	76.39
Mean single sequence MFE	-42.86
Consensus MFE	-19.79
Energy contribution	-20.27
Covariance contribution	0.48
Combinations/Pair	1.35
Mean z-score	-1.90
Structure conservation index	0.46
SVM decision value	0.00
SVM RNA-class probability	0.535705
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5271483 120 + 27905053
CCACGAUCGGCGGUGCAAACUCGGCGGCCAGCCUGCUAGUCAACGGCACCGGCAUCAAUUUGUCCAUCAAUCUGGGCUCACCCAAUCCGGCGCCCAAUCUAGCGGUUGCCACACAGCUGC
.........(((((((.......))(((.((((.(((((.....(((.((((.........(((((......))))).........)))).)))....)))))))))))).....))))) ( -42.57)
>DroVir_CAF1 44732 120 + 1
CGGCCAUCGGCGGUGCGGGUACUGCAACCAGUCUGUUGGUCAAUGGCGCAGGCAUUAAUCUAUCCCUCAACCUGGGCUCACCUAACCCAGCGCCCAAUCUGGCAGUUGCCACACAAUUGC
.(((((.(((((((((((...)))).))).).))).)))))...((((((((.((......)).))).....((((.........))))))))).......(((((((.....))))))) ( -38.20)
>DroGri_CAF1 54967 120 + 1
CUGCAAUCGGUGGUGCGGCAACCGCAGCCAGUCUUUUGGUCAAUGGCACCGGCAUCAACUUAUCCCUCAAUUUGGGCGCGCCAAAUCCGGCGCCAAAUCUAGCUGUUGCCAAUCAGCUGC
..(((...(.((((..((((((.((.(((((....)))))...((((.((((...........(((.......)))..........)))).))))......)).)))))).)))).)))) ( -40.20)
>DroWil_CAF1 55779 120 + 1
CAUCGAUUGGCGGCGCUGGCUCCGCAUCCAGUGUCCUAGUCAAUGGUACUGGCAUCAAUUUGUCCCUCAAUCUGGGUGCUCCGAAUCCUGCGCCCAAUCUAGCAGUUGCCACACAAUUGC
(((.((((((.((((((((........)))))))))))))).))).....((((......))))........(((((((..........))))))).....(((((((.....))))))) ( -41.40)
>DroMoj_CAF1 46290 120 + 1
CGGCCAUCGGCGGCGCCGGCACUGCGGCCAGCCUCCUGGUCAGCAAUGCGGGCAUCAACUUGUCCCUCAACUUGAGCGCCCCCAAUCCGACGCCCAACCUGGCGUUUGCCACACAGCUGU
.(((....((.((((((.(((.(((((((((....)))))).))).))).))).((((.(((.....))).))))..))).)).....((((((......)))))).))).......... ( -49.50)
>DroAna_CAF1 42620 120 + 1
CAACGAUCGGCGGCACCAGCUCCGCUGCCAGCCUGCUAGUCAACGGCACCGGCAUCAACUUGUCUAUCAACCUGGGCGCCCCCAAUCCGGCGCCCAAUCUAGCGGUUGCCACUCAACUCC
....(((..(((((..((((...))))...))).))..)))...((((((((((......))))........((((((((........)))))))).......)).)))).......... ( -45.30)
>consensus
CAGCGAUCGGCGGCGCCGGCACCGCAGCCAGCCUGCUAGUCAACGGCACCGGCAUCAACUUGUCCCUCAACCUGGGCGCACCCAAUCCGGCGCCCAAUCUAGCGGUUGCCACACAACUGC
.........((((........))))...((((......(.((((.((...((((......))))........(((((((..........))))))).....)).)))).).....)))). (-19.79 = -20.27 +   0.48)

alignment

secondary structure

dotplot

Window 1

Location	5,271,523 – 5,271,628
Length	105
Sequences	6
Columns	113
Reading direction	forward
Mean pairwise identity	78.38
Mean single sequence MFE	-32.22
Consensus MFE	-22.39
Energy contribution	-22.17
Covariance contribution	-0.22
Combinations/Pair	1.33
Mean z-score	-2.04
Structure conservation index	0.69
SVM decision value	1.33
SVM RNA-class probability	0.943254
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5271523 105 + 27905053
CAACGGCACCGGCAUCAAUUUGUCCAUCAAUCUGGGCUCACCCAAUCCGGCGCCCAAUCUAGCGGUUGCCACACAGCUGCUCGAGCAUAUUAAGGUUAG---ACUUG-----G
....(((.((((.........(((((......))))).........)))).)))...((.((((((((.....)))))))).))......((((.....---.))))-----. ( -32.17)
>DroVir_CAF1 44772 106 + 1
CAAUGGCGCAGGCAUUAAUCUAUCCCUCAACCUGGGCUCACCUAACCCAGCGCCCAAUCUGGCAGUUGCCACACAAUUGCUUGAGCACAUUAAGGUAUG---UCAUUU---U-
.(((((((.(((.((......)).)))).((((((((.(..........).))))..((.((((((((.....)))))))).))........))))..)---))))).---.- ( -27.20)
>DroGri_CAF1 55007 109 + 1
CAAUGGCACCGGCAUCAACUUAUCCCUCAAUUUGGGCGCGCCAAAUCCGGCGCCAAAUCUAGCUGUUGCCAAUCAGCUGCUGGAGCACAUUAAGGUACC---GUCUCCUACU-
.((((((.(((((..........(((.......))).(((((......))))).......(((((........)))))))))).)).)))).(((....---....)))...- ( -34.70)
>DroEre_CAF1 47580 109 + 1
CAACGGCACCGGCAUCAAUUUGUCCAUCAAUCUGGGCUCACCCAAUCCGGCGCCCAAUCUGGCGGUUGCCACACAGCUGCUCGAGCAUAUUAAGGUUAG---ACCUGCGAAU-
....(((.((((.........(((((......))))).........)))).)))...((.((((((((.....)))))))).))........(((....---.)))......- ( -32.87)
>DroWil_CAF1 55819 108 + 1
CAAUGGUACUGGCAUCAAUUUGUCCCUCAAUCUGGGUGCUCCGAAUCCUGCGCCCAAUCUAGCAGUUGCCACACAAUUGCUCGAGCAUAUUAAGGUAAAGUGAUUUG-----G
(((...((((((((......))))(((.(((.(((((((..........))))))).((.((((((((.....)))))))).))....))).)))...))))..)))-----. ( -29.90)
>DroAna_CAF1 42660 106 + 1
CAACGGCACCGGCAUCAACUUGUCUAUCAACCUGGGCGCCCCCAAUCCGGCGCCCAAUCUAGCGGUUGCCACUCAACUCCUUGAGCAUAUUAAGGUAAGG--AAUUA-----U
....((((((((((......))))........((((((((........)))))))).......)).))))..((....((((((.....))))))....)--)....-----. ( -36.50)
>consensus
CAACGGCACCGGCAUCAAUUUGUCCAUCAAUCUGGGCGCACCCAAUCCGGCGCCCAAUCUAGCGGUUGCCACACAACUGCUCGAGCAUAUUAAGGUAAG___ACUUG______
....(((.((((.........((((........)))).........)))).)))...((.((((((((.....)))))))).))............................. (-22.39 = -22.17 +  -0.22)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:20:43 2006